RUM (RNA-Seq Unified Mapper) is a pipeline to map Illumina RNA-seq data. The RUM algorithm Bowtie to map the reads onto a genome and to a transcriptome database. It uses BLAT for mapping against the genome and merges all three mappings into one. Note that the usage of BLAT requires a separate license.
RNA-seq
Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA "Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)." Bioinformatics. 2011 Sep 15;27(18):2518-28. Epub 2011 Jul 19. https://doi.org/10.1093/bioinformatics/btr427
PMID: 21775302
PMCID: PMC3167048
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